Biology subjects

Mack, K. L.

Publications and source records attributed to Mack, K. L..

11 recordsLinked to original sources

bioRxiv2025

Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas

Alternative splicing is a major driver of transcriptome and proteome variation, but the role of alternative splicing in regulatory evolution remains understudied. Alternative splicing can also contribute to phenotypic plasticity, which may be critical when taxa colonize new environments. Here, we investigate variation in alternative splicing among new wild-derived strains of mice from different climates in the Americas on both a standard and high-fat diet. We show that alternative splicing is widespread and highly context-dependent. Comparisons between strains on different diets revealed abundant gene-by-environment interactions affecting alternative splicing, with most genes showing strain- and sex-specific diet responses. More often than not, genes that were differentially spliced between strains were not differentially expressed, adding to evidence that the two regulatory mechanisms often act independently. Moreover, differentially spliced genes were more widely expressed across tissues but also less central to biological networks than differentially expressed genes, suggesting differences in pleiotropic constraint. Importantly, divergence in alternative splicing was found to be predominantly driven by cis- regulatory changes. However, trans changes affecting splicing make be central to plasticity as they were impacted more by environmental variation. Finally, we performed scans for selection and found that, while genes with splicing divergence more often co-localized with genomic outliers associated with metabolic traits, they were not enriched for genomic outliers. Overall, our results provide evidence that alternative splicing plays an important role in gene regulation in house mice, contributing to adaptation and plasticity.

evolutionary biology↗

bioRxiv2024

Gene-by-environment interactions and adaptive body size variation in mice from the Americas

The relationship between genotype and phenotype is often mediated by the environment. Moreover, gene-by-environment (GxE) interactions can contribute to variation in phenotypes and, in turn, fitness. Nevertheless, understanding the impact of GxE interactions in wild systems remains challenging. In the last 500 years, house mice have invaded the Americas. Despite their short residence time, there is evidence of rapid climate adaptation, including shifts in body size and aspects of metabolism with latitude. Previous studies in this system have identified candidate genes for metabolic adaptation using selection scans, however, environmental variation in diet as well as GxE interactions affecting metabolism are likely important factors in shaping body mass variation in wild populations. Here, we investigate the role of the environment and GxE interactions in shaping adaptive phenotypic variation with an experimental manipulation of diet. Using new locally adapted inbred strains from North and South America, we evaluated response to a high-fat diet, finding that sex, strain, diet, and the interaction between strain and diet contribute significantly to variation in aspects of body size. We also found that transcriptional response to diet is largely strain-specific, indicating that GxE interactions affecting gene expression are pervasive. Next, we used crosses between strains from contrasting climates (New York x Brazil and New York x Florida) to characterize gene expression regulatory divergence on a standard breeder diet and on a high-fat diet. We found that gene regulatory divergence is often condition-specific, particularly for trans-acting changes. Finally, we find evidence for lineage-specific selection on cis-regulatory variation involved in diverse processes, including lipid metabolism. Overlap with scans for selection identified candidate genes for environmental adaptation with diet-specific effects. Together, our results underscore the importance of environmental variation and GxE interactions to adaptive variation in complex traits.

evolutionary biology↗

bioRxiv2024

Defining a small-molecule stimulator of the human Hsp70-disaggregase system with selectivity for DnaJB proteins

Hsp70, Hsp40, and Hsp110 form a human protein-disaggregase system that solubilizes and reactivates proteins trapped in aggregated states. However, this system fails to maintain proteostasis in fatal neurodegenerative diseases. Here, we potentiate the human Hsp70-disaggregase system pharmacologically. By scouring a collection of dihydropyrimidines, we disambiguate a small molecule that specifically stimulates the Hsp70-disaggregase system against disordered aggregates and -synuclein fibrils. The newly identified lead compound stimulates the disaggregase activity of multiple active human Hsp70, Hsp40, Hsp110 chaperone sets, with selectivity for combinations that include DnaJB1 or DnaJB4 as the Hsp40. We find that the relative stoichiometry of Hsp70, Hsp40, and Hsp110 dictates disaggregase activity. Remarkably, our lead compound shifts the composition of active chaperone stoichiometries by preferentially activating combinations with lower DnaJB1 concentrations. Our findings unveil a small molecule that stimulates the Hsp70-disaggregase system, even at suboptimal chaperone stoichiometries, which could be developed for the treatment of neurodegenerative diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/575109v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1f1b574org.highwire.dtl.DTLVardef@1bfd3aborg.highwire.dtl.DTLVardef@e191e3org.highwire.dtl.DTLVardef@130d19c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks

Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are enriched in genomic regions associated with marine-freshwater divergence, supporting an important role for cis-regulatory differences in adaptive evolution of sticklebacks. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes and supports a fundamental role for cis-regulatory changes in rapid adaptation to new environments.

evolutionary biology↗

bioRxiv2022

Allele-specific expression reveals genetic drivers of tissue regeneration in mice

In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, "super-healer" MRL mice have the unusual ability to regenerate ear punch wounds, yet the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we use allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major wound cell populations, we identified extensive strain- and tissue- specific cis-regulatory divergence associated with differences in healing outcomes. Genes with cis-regulatory differences specifically in fibroblasts were associated with wound healing phenotypes and pathways, and were enriched near genetic markers associated with ear-healing in a genetic cross. Finally, we demonstrated that one of these genes, Cfh, could be applied ectopically to accelerate wound repair and induce regeneration in typically fibrotic wounds. Overall, our results provide insight into the molecular drivers of regeneration in MRL mice with potential clinical implications.

genomics↗

bioRxiv2022

Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

Changes in gene expression are proposed to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene regulation in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5-10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we discovered a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and non-genetic mechanisms underlying the establishment of populations in new environments. Significance StatementGene expression variation is shaped by both genetic and environmental effects, yet these two factors are rarely considered together in the context of adaptive evolution. We studied environmental influences on gene regulatory evolution in temperate and tropical house mice in cold and warm laboratory environments. We discovered that genetic effects in the form of cis-regulatory divergence were pervasive and largely insensitive to the environment. Many of these genetic effects are under selection and are associated with genes that affect body size, suggesting cis-regulatory changes as a possible mechanism for adaptive body size evolution. We also discovered many trans-effects controlling expression plasticity, demonstrating the importance of both genetic and non-genetic changes associated with adaptation over short timescales (a few hundred generations).

evolutionary biology↗

bioRxiv2021

Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents

Desert specialization has arisen multiple times across rodents and is often associated with a suite of convergent phenotypes, including modification of the kidneys to mitigate water loss. However, the extent to which phenotypic convergence in desert rodents is mirrored at the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes for three pairs of rodent species to search for convergence in gene expression and amino acid sequence associated with adaptation to deserts. We conducted phylogenetically-independent comparisons between a desert specialist and a non-desert relative in three families representing [~]70 million years of evolution. Overall, patterns of gene expression faithfully recapitulated the phylogeny of these six taxa. However, we found that 8.6% of all genes showed convergent patterns of expression evolution between desert and non-desert taxa, a proportion that is much higher than expected by chance. In addition to these convergent changes, we observed many species-pair specific changes in gene expression indicating that different instances of adaptation to deserts include a combination of unique and shared changes. Patterns of protein evolution revealed a small number of genes showing evidence of positive selection, the majority of which did not show convergent changes in gene expression. Overall, our results suggest convergent changes in gene regulation play a primary role in the complex trait of desert adaptation in rodents.

evolutionary biology↗

bioRxiv2021

Opposing roles of p38α phosphorylation and arginine methylation in driving TDP-43 proteinopathy.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder typically characterized by insoluble inclusions of hyperphosphorylated TDP-43. The mechanisms underlying toxic TDP-43 accumulation are not understood. Persistent activation of p38 mitogen-activated protein kinase (MAPK) is implicated in ALS. However, it is unclear how p38 MAPK affects TDP-43 proteinopathy. Here, we demonstrate that inhibition of p38 MAPK reduces pathological TDP-43 phosphorylation, aggregation, cytoplasmic mislocalization, and neurotoxicity. We establish that p38 MAPK phosphorylates TDP-43 at pathological serine 409/410 (S409/S410) and serine 292 (S292), which reduces TDP-43 liquid-liquid phase separation (LLPS) but allows pathological TDP-43 aggregation. Moreover, we show that protein arginine methyltransferase 1 methylates TDP-43 at R293. Importantly, S292 phosphorylation reduces R293 methylation, and R293 methylation reduces S409/S410 phosphorylation. R293 methylation permits TDP-43 LLPS and reduces pathological TDP-43 aggregation. Thus, strategies to reduce p38-mediated TDP-43 phosphorylation and promote R293 methylation could have therapeutic utility for ALS and related TDP-43 proteinopathies.

molecular biology↗

bioRxiv2020

Tuning Hsp104 specificity to selectively detoxify alpha-synuclein

Hsp104 is an AAA+ protein disaggregase that solubilizes and reactivates proteins trapped in aggregated states. We have engineered potentiated Hsp104 variants to mitigate toxic misfolding of -synuclein, TDP-43, and FUS implicated in fatal neurodegenerative disorders. Though potent disaggregases, these enhanced Hsp104 variants lack substrate specificity, and can have unfavorable off-target effects. Here, to lessen off-target effects, we engineer substrate-specific Hsp104 variants. By altering Hsp104 pore loops that engage substrate, we disambiguate Hsp104 variants that selectively suppress -synuclein toxicity but not TDP-43 or FUS toxicity. Remarkably, -synuclein-specific Hsp104 variants emerge that mitigate -synuclein toxicity via distinct ATPase-dependent mechanisms, involving -synuclein disaggregation or detoxification of -synuclein conformers without disaggregation. Importantly, both types of -synuclein-specific Hsp104 variant reduce dopaminergic neurodegeneration in a C. elegans model of Parkinsons disease more effectively than non-specific variants. We suggest that increasing the substrate specificity of enhanced disaggregases could be applied broadly to tailor therapeutics for neurodegenerative disease.

bioengineering↗

bioRxiv2020

Plasticity in gene expression facilitates invasion of the desert environment in house mice

Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied the evolved and plastic responses to water stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments. Using a full sib design, we measured organismal phenotypes and gene expression under normal (hydrated) and water stressed (dehydrated) conditions. After many generations in the lab, mice from the desert consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis. Under water stress, desert mice lost less weight than non-desert mice, and desert mice exhibited differences in blood chemistry related to osmoregulatory function. Gene expression in the kidney revealed evolved differences between mice from different environments as well as plastic responses between hydrated and dehydrated mice. Desert mice showed reduced gene expression plasticity under water stress compared to non-desert mice. Importantly, the non-desert mice generally showed shifts towards desert-like expression under water stress, consistent with adaptive plasticity. Finally, patterns of gene expression identified several candidate genes for adaptation to the desert, including Aqp1 and Apoe. These findings provide evidence for local adaptation in a recently introduced species and suggest that adaptive plasticity may have facilitated the colonization of the desert environment.

evolutionary biology↗

bioRxiv2020

Repeated evolution of circadian clock dysregulation in cavefish populations

Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting environments with arrhythmic days, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Here we demonstrate that the cave environment has led to the repeated disruption of the biological clock across multiple populations of Mexican cavefish, with the circadian transcriptome showing widespread reductions in rhythmicity and changes to the timing of the activation/repression of genes in the core pacemaker. Then, we investigate the function of two genes with decreased rhythmic expression in cavefish. Mutants of these genes phenocopy reductions in sleep seen in multiple cave populations, suggesting a link between circadian dysregulation and sleep reduction. Altogether, our results reveal that evolution in an arrhythmic environment has resulted in dysregulation to the biological clock across multiple populations by diverse molecular mechanisms.

evolutionary biology↗